Package picard.fingerprint
Class LiftOverHaplotypeMap
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.fingerprint.LiftOverHaplotypeMap
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public class LiftOverHaplotypeMap extends CommandLineProgram
Liftover SNPs in HaplotypeMaps from one reference to another
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Field Summary
Fields Modifier and Type Field Description File
CHAIN
File
INPUT
static int
LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
File
OUTPUT
File
SEQUENCE_DICTIONARY
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description LiftOverHaplotypeMap()
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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INPUT
@Argument(doc="Haplotype database to be lifted over.", shortName="I") public File INPUT
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OUTPUT
@Argument(doc="Where to write lifted-over haplotype database.", shortName="O") public File OUTPUT
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SEQUENCE_DICTIONARY
@Argument(doc="Sequence dictionary to write into the output haplotype database. (Any file from which a dictionary is extractable.)", shortName="SD") public File SEQUENCE_DICTIONARY
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CHAIN
@Argument(doc="Chain file that guides LiftOver. (UCSC format)") public File CHAIN
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LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
public static final int LIFTOVER_FAILED_FOR_ONE_OR_MORE_SNPS
- See Also:
- Constant Field Values
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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